Physical Sciences and Mathematics Commons^™

Adaptive Global Optimization Algorithms, William Phillips

Dissertations

Global optimization is concerned with finding the minimum value of a function where many local minima may exist. The development of a global optimization algorithm may involve using information about the target function (e.g., differentiability) and functions based on statistical models to better the worst case time complexity and expected error of similar deterministic algorithms.

Recent algorithms are investigated, new ones proposed and their performance is analyzed. Minimum, maximum and average case error bounds for the algorithms presented are derived. Software architecture implemented with MATLAB and Java is presented and experimental results for the algorithms are displayed.

The graphical capabilities …

Enabling Virtualization Technologies For Enhanced Cloud Computing, Kashifuddin Qazi

Dissertations

Cloud Computing is a ubiquitous technology that offers various services for individual users, small businesses, as well as large scale organizations. Data-center owners maintain clusters of thousands of machines and lease out resources like CPU, memory, network bandwidth, and storage to clients. For organizations, cloud computing provides the means to offload server infrastructure and obtain resources on demand, which reduces setup costs as well as maintenance overheads. For individuals, cloud computing offers platforms, resources and services that would otherwise be unavailable to them.

At the core of cloud computing are various virtualization technologies and the resulting Virtual Machines (VMs). Virtualization …

Rice And Mouse Quantitative Phenotype Prediction In Genome-Wide Association Studies With Support Vector Regression, Abdulrhman Fahad M. Aljouie

Theses

Quantitative phenotypes prediction from genotype data is significant for pathogenesis, crop yields, and immunity tests. The scientific community conducted many studies to find unobserved quantitative phenotype high predictive ability models. Early genome-wide association studies (GWAS) focused on genetic variants that are associated with disease or phenotype, however, these variants manly covers small portion of the whole genetic variance, and therefore, the effectiveness of predictions obtained using this information may possibly be circumscribed [ 1 ].

Instead, this study shows prediction ability from whole genome single nucleotide polymorphisms (SNPs) data of 1940 genotyped stoke mouse with - 12k SNPs, and 413 …

Cancer Risk Prediction With Next Generation Sequencing Data Using Machine Learning, Nihir Patel

Theses

The use of computational biology for next generation sequencing (NGS) analysis is rapidly increasing in genomics research. However, the effectiveness of NGS data to predict disease abundance is yet unclear. This research investigates the problem in the whole exome NGS data of the chronic lymphocytic leukemia (CLL) available at dbGaP. Initially, raw reads from samples are aligned to the human reference genome using burrows wheeler aligner. From the samples, structural variants, namely, Single Nucleotide Polymorphism (SNP) and Insertion Deletion (INDEL) are identified and are filtered using SAMtools as well as with Genome Analyzer Tool Kit (GATK). Subsequently, the variants are …

The Cantor Trilogy, Harun Šiljak

Journal of Humanistic Mathematics

The Cantor trilogy is a mathematical dystopia featuring JHM as an important part of that world... at least to humans.

My Finite Field, Matthew Schroeder

Journal of Humanistic Mathematics

A love poem written in the language of mathematics.

Prisoner's Dilemma, Raymond N. Greenwell

Journal of Humanistic Mathematics

No abstract provided.

Book Review: Love And Math: The Heart Of Hidden Reality By Edward Frenkel, Emily R. Grosholz

Journal of Humanistic Mathematics

This review traces Edward Frenkel’s attempt to convey the excitement of mathematical research to a popular audience. In his expositions and explanations of his own research program, he shows how processes of mathematical discovery depend on the juxtaposition of various iconic and symbolic modes of representation as disparate fields of research are brought together in the service of problem solving. And he shows how crucial the encouragement of various older mathematicians was to his own development, as they guided his choice of problems, and served as inspiration.

Abscissas And Ordinates, David Pierce

Journal of Humanistic Mathematics

In the manner of Apollonius of Perga, but hardly any modern book, we investigate conic sections as such. We thus discover why Apollonius calls a conic section a parabola, an hyperbola, or an ellipse; and we discover the meanings of the terms abscissa and ordinate. In an education that is liberating and not simply indoctrinating, the student of mathematics will learn these things.

The Symbolic And Mathematical Influence Of Diophantus's Arithmetica, Cyrus Hettle

Journal of Humanistic Mathematics

Though it was written in Greek in a center of ancient Greek learning, Diophantus's Arithmetica is a curious synthesis of Greek, Egyptian, and Mesopotamian mathematics. It was not only one of the first purely number-theoretic and algebraic texts, but the first to use the blend of rhetorical and symbolic exposition known as syncopated mathematics. The text was influential in the development of Arabic algebra and European number theory and notation, and its development of the theory of indeterminate, or Diophantine, equations inspired modern work in both abstract algebra and computer science. We present, in this article, a selection of problems …

Love Games: A Game-Theory Approach To Compatibility, Kerstin Bever, Julie Rowlett

Journal of Humanistic Mathematics

In this note, we present a compatibility test with a rigorous mathematical foundation in game theory. The test must be taken separately by both partners, making it difficult for either partner alone to control the outcome. To introduce basic notions of game theory we investigate a scene from the film "A Beautiful Mind" based on John Nash's life and Nobel-prize-winning theorem. We recall this result and reveal the mathematics behind our test. Readers may customize and modify the test for more accurate results or to evaluate interpersonal relationships in other settings, not only romantic. Finally, we apply Dyson's and Press's …

On The Persistence And Attrition Of Women In Mathematics, Katrina Piatek-Jimenez

Journal of Humanistic Mathematics

The purpose of this study was to investigate what motivates women to choose mathematics as an undergraduate major and to further explore what shapes their future career goals, paying particular attention to their undergraduate experiences and their perceptions of the role of gender in these decisions. A series of semi-structured, individual interviews were conducted with twelve undergraduate women mathematics majors who were attending either a large public university or a small liberal arts college. This study found that strong mathematical identities and enjoyment of mathematics heavily influenced their decisions to major in mathematics. At the career selection stage, these women …

The Ancestral Activation Promiscuity Of Adp-Glucose Pyrophosphorylases From Oxygenic Photosynthetic Organisms, Misty L. Kuhn, Carlos M. Figueroa, Alberto A. Iglesias, Miguel Ballicora

Miguel A Ballicora

Background ADP-glucose pyrophosphorylase (ADP-Glc PPase) catalyzes the first committed step in the synthesis of glycogen in bacteria and starch in algae and plants. In oxygenic photosynthetic organisms, ADP-Glc PPase is mainly activated by 3-phosphoglycerate (3-PGA) and to a lesser extent by other metabolites. In this work, we analyzed the activation promiscuity of ADP-Glc PPase subunits from the cyanobacterium Anabaena PCC 7120, the green alga Ostreococcus tauri, and potato (Solanum tuberosum) tuber by comparing a specificity constant for 3-PGA, fructose-1,6-bisphosphate (FBP), fructose-6-phosphate, and glucose-6-phosphate. Results The 3-PGA specificity constant for the enzymes from Anabaena (homotetramer), O. tauri, and potato tuber was …

Investigating The Electrostatic Role Of A Critical Arginine For The Catalysis Of E. Coli Adp-Glucose Pyrophosphorylase, Angela Mahaffey, Saleh Aiyash, Miguel Ballicora, Ligin Solamen

Miguel A Ballicora

ADP-glucose pyrophosphorylase (ADP-Glc PPase) is the regulatory enzyme of the pathway for starch synthesis in plants and glycogen in mammals and enteric bacteria. It exists as a 200 kDa homotetramer (α4) in enteric bacteria, and as a heterotetramer (α2β2) in plants. In both in vivo and in vitro the substrates (Glucose 1-Phosphate; Glc-1P and Adenosine 5'-Triphosphate; ATP) are converted into a glucose donor ADP-Glucose and a pyrophosphate (PPi) via the ADP-Glc PPase enzyme. It has been noted that some residues are conserved in homotetrameric bacterial ADP-Glc PPases, but are not in some plant forms. One of them is Arginine-32 (R32) …

A Study Of Photon Trapping And The Ac Stark Effect In Photonic Crystals And Dispersive Materials, Iftekharul Haque

Electronic Thesis and Dissertation Repository

In this thesis, we study light-matter interaction in the contexts of coherent population trapping (CPT) and the ac Stark effect in nanoparticles embedded (doped) in two important classes of reservoirs -- photonic crystals and dispersive materials. These materials have gaps in their energy spectra and are studied widely due to their unusual optical properties and potential for novel applications. We consider that the reservoirs are doped with an ensemble of five-level nanoparticles, each with a single Λ core (consisting of a lower doublet and an upper energy level), which interact with both the host reservoir and external radiation fields. We …

A Xenon Bubble Chamber For Direct Dark Matter Detection, Matthew M. Szydagis

Physics Faculty Scholarship

With the lack of discovery of WIMPs at high mass, and hints of signals at low masses, it is becoming increasingly important for direct dark matter detectors to set low thresholds. With a hypothetically completely tuneable threshold based on pressure and temperature, a bubble chamber could be the ideal detector to search for sub-GeV WIMPs and other light exotica. However, this technology has its own drawbacks, such as an unknown recoil energy on an event-by-event basis. By combining this technology with that of the xenon time-projection chamber, however, the strengths of both of these approaches are merged, leading to a …

Optimal Dynamic Treatments In Resource-Limited Settings, Alexander R. Luedtke, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

A dynamic treatment rule (DTR) is a treatment rule which assigns treatments to individuals based on (a subset of) their measured covariates. An optimal DTR is the DTR which maximizes the population mean outcome. Previous works in this area have assumed that treatment is an unlimited resource so that the entire population can be treated if this strategy maximizes the population mean outcome. We consider optimal DTRs in settings where the treatment resource is limited so that there is a maximum proportion of the population which can be treated. We give a general closed-form expression for an optimal stochastic DTR …

Hd 207651: A Composite Spectrum Triple System, Francis C. Fekel

Information Systems and Engineering Management Research Publications

From numerous radial velocities obtained at KPNO and Fairborn Observatory, we have determined the orbital elements of the composite spectrum triple system HD 207651. This system consists of a broad-lined A8 V star and an unseen M dwarf companion in a 1.470739 days orbit. Variations of the center-of-mass velocity of this short-period system and velocity variations of a narrow-lined F7: V star have an orbital period of 724.1 days or 1.98 yr and an eccentricity of 0.39. The revised Hipparcos parallax, corresponding to a distance of 255 pc, appears to be too small to yield consistent properties. Instead, we adopt …

Emphasizing The Entire Research Process Throughout The Curriculum: The Next Step In Real Data Integration In Introductory Statistics Courses, Nathan L. Tintle

Faculty Work Comprehensive List

Access blog post at publisher's site:

https://www.causeweb.org/sbi/?p=617

A Defeasible Reasoning Framework For Human Mental Workload Representation And Assessment, Luca Longo

Conference papers

Human mental workload (MWL) has gained importance in the last few decades as an important design concept. It is a multifaceted complex construct mainly applied in cognitive sciences and has been defined in many different ways. Although measuring MWL has potential advantages in interaction and interface design, its formalisation as an operational and computational construct has not sufficiently been addressed. This research contributes to the body of knowledge by providing an extensible framework built upon defeasible reasoning, and implemented with argumentation theory (AT), in which MWL can be better defined, measured, analysed, explained and applied in different human–computer interactive contexts. …

Gut Microbiota-Dependent Trimethylamine N-Oxide (Tmao) Pathway Contributes To Both Development Of Renal Insufficiency And Mortality Risk In Chronic Kidney Disease, W.H. Wilson Tang, Zeneng Wang, David J. Kennedy, Yuping Wu, Jennifer A. Buffa, Brendan Agatisa Boyle, Xinmin S. Li, Bruce S. Levison, Stanley L. Hazen

Mathematics and Statistics Faculty Publications

RATIONALE: Trimethylamine-N-oxide (TMAO), a gut microbial-dependent metabolite of dietary choline, phosphatidylcholine (lecithin), and l-carnitine, is elevated in chronic kidney diseases (CKD) and associated with coronary artery disease pathogenesis. OBJECTIVE: To both investigate the clinical prognostic value of TMAO in subjects with versus without CKD, and test the hypothesis that TMAO plays a direct contributory role in the development and progression of renal dysfunction. METHODS AND RESULTS: We first examined the relationship between fasting plasma TMAO and all-cause mortality over 5-year follow-up in 521 stable subjects with CKD (estimated glomerular filtration rate, <60 mL/min per 1.73 m(2)). Median TMAO level among CKD subjects was 7.9 μmol/L (interquartile range, 5.2-12.4 μmol/L), which was markedly higher (P<0.001) than in non-CKD subjects (n=3166). Within CKD subjects, higher (fourth versus first quartile) plasma TMAO level was associated with a 2.8-fold increased mortality risk. After adjustments for traditional risk factors, high-sensitivity C-reactive protein, estimated glomerular filtration rate, elevated TMAO levels remained predictive of 5-year mortality risk (hazard ratio, 1.93; 95% confidence interval, 1.13-3.29; P<0.05). TMAO provided significant incremental prognostic value (net reclassification index, 17.26%; P<0.001 and differences in area under receiver operator characteristic curve, 63.26% versus 65.95%; P=0.036). Among non-CKD subjects, elevated TMAO levels portend poorer prognosis within cohorts of high and low cystatin C. In animal models, elevated dietary choline or TMAO directly led to progressive renal tubulointerstitial fibrosis and dysfunction. CONCLUSIONS: Plasma TMAO levels are both elevated in patients with CKD and portend poorer long-term survival. Chronic dietary exposures that increase TMAO directly contributes to progressive renal fibrosis and dysfunction in animal models.

Synthesis And Characterization Of Polymer (Sulfonated Poly-Ether-Ether-Ketone) Based Nanocomposite (H-Boron Nitride) Membrane For Hydrogen Storage, R. Muthu Nareth, S. Rajashabla, Ramaiyan Navaneetha Kannan

All Physics Faculty Publications

The development of light weight and compact hydrogen storage materials is still prerequisite to fuel-cell technology to be fully competitive. The present experimental study reports the hydrogen storage capability of sulfonated poly-ether-ether-ketone (SPEEK)-hexagonal boron nitride (h-BN) (SPEEK-h-BN) nanocomposite membranes. The nanocomposite membranes are prepared by considering various amount of h-BN (0, 1, 3 and 5 wt. %) by phase inversion technique. The degree of sulfonation of the PEEK (SPEEK) is found to be 65% by Proton Nuclear Magnetic Resonance (¹H NMR) spectroscopy. Hydrogen adsorption studies have been carried out using a Seiverts-like hydrogenation setup. The membranes are characterized …

Synthesis Of Dinucleoside Acylphosphonites By Phosphonodiamidite Chemistry And Investigation Of Phosphorus Epimerization, William H. Hersh

Publications and Research

The reaction of the diamidite, (iPr2N)2PH, with acyl chlorides proceeds with the loss of HCl to give the corresponding acyl diamidites, RC(O)P(N(iPr)2)2 (R = Me (7), Ph (9)), without the intervention of sodium to give a phosphorus anion. The structure of 9 was confirmed by single-crystal X-ray diffraction. The coupling of the diamidites 7 and 9 with 5′-O-DMTr-thymidine was carried out with N-methylimidazolium triflate as the activator to give the monoamidites 3′-O-(P(N(iPr)2)C(O)R)-5′-O-DMTr-thymidine, and further coupling with 3′-O-(tert-butyldimethylsilyl)thymidine was carried out with activation by pyridinium trifluoroacetate/Nmethylimidazole. The new dinucleoside acylphosphonites could be further oxidized, hydrolyzed to the H-phosphonates, and sulfurized to …

Lorentz Violation With An Antisymmetric Tensor, Brett Altschul, Quentin G. Bailey, V. Alan Kostelecky

Quentin Bailey

Field theories with spontaneous Lorentz violation involving an antisymmetric 2-tensor are studied. A general action including nonminimal gravitational couplings is constructed, and features of the Nambu- Goldstone and massive modes are discussed. Minimal models in Minkowski spacetime exhibit dualities with Lorentz-violating vector and scalar theories. The post-Newtonian expansion for nonminimal models in Riemann spacetime involves qualitatively new features, including the absence of an isotropic limit. Certain interactions producing stable Lorentz-violating theories in Minkowski spacetime solve the renormalization-group equations in the tadpole approximation.

Lorentz-Violating Gravitoelectromagnetism, Quentin G. Bailey

Quentin Bailey

The well-known analogy between a special limit of general relativity and electromagnetism is explored in the context of the Lorentz-violating standard-model extension. An analogy is developed for the minimal standard-model extension that connects a limit of the CPT-even component of the electromagnetic sector to the gravitational sector. We show that components of the post-Newtonian metric can be directly obtained from solutions to the electromagnetic sector. The method is illustrated with specific examples including static and rotating sources. Some unconventional effects that arise for Lorentz-violating electrostatics and magnetostatics have an analog in Lorentz-violating post-Newtonian gravity. In particular, we show that even …

Limits On Violations Of Lorentz Symmetry From Gravity Probe B, Quentin G. Bailey, Ryan D. Everett, James M. Overduin

Quentin Bailey

Generic violations of Lorentz symmetry can be described by an effective field theory framework that contains both general relativity and the Standard Model of particle physics called the Standard-Model extension (SME). We obtain new constraints on the gravitational sector of the SME using recently published final results from Gravity Probe B. These include for the first time an upper limit at the 10_3 level on the time-time component of the new tensor field responsible for inducing local Lorentz violation in the theory, and an independent limit at the 10_7 level on a combination of components of this tensor field.

Time-Delay And Doppler Tests Of The Lorentz Symmetry Of Gravity, Quentin G. Bailey

Quentin Bailey

Modifications to the classic time-delay effect and Doppler shift in general relativity (GR) are studied in the context of the Lorentz-violating standard-model extension (SME). We derive the leading Lorentz- violating corrections to the time-delay and Doppler shift signals, for a light ray passing near a massive body. It is demonstrated that anisotropic coefficients for Lorentz violation control a time-dependent behavior of these signals that is qualitatively different from the conventional case in GR. Estimates of sensitivities to gravity-sector coefficients in the SME are given for current and future experiments, including the recent Cassini solar conjunction experiment.

Catching Relativity Violations With Atoms, Quentin G. Bailey

Quentin Bailey

A Viewpoint on: Atom interferometry tests of local Lorentz invariance in gravity and electrodynamics Keng-Yeow Chung, Sheng-wey Chiow, Sven Herrmann, Steven Chu and Holger Müller Phys. Rev. D 80, 016002 (2009) – Published July 6, 2009.

Light-Bending Tests Of Lorentz Invariance, Quentin G. Bailey, Rhondale Tso

Quentin Bailey

Classical light-bending is investigated for weak gravitational fields in the presence of hypothetical local Lorentz violation. Using an effective field theory framework that describes general deviations from local Lorentz invariance, we derive a modified deflection angle for light passing near a massive body. The results include anisotropic effects not present for spherical sources in General Relativity as well as Weak Equivalence Principle violation. We develop an expression for the relative deflection of two distant stars that can be used to analyze data in past and future solar-system observations. The measurement sensitivities of such tests to coefficients for Lorentz violation are …

Controls On Bed Erodibility In The York River Estuary, C. T. Friedrichs, Grace M. Cartwright, R. J. Diaz, P. J. Dickhut

Presentations

No abstract provided.